CTS2 Development Framework In Action

Schedule

• Why develop against CTS2?
• JSON format
• Searching
• ChangeSet workflow
• Mapping view/create
• Bioportal integration

Why develop against CTS2?

CTS2 Development Framework
supports XML, JSON, and JSONP
• JSONP is useful in avoiding Cross-Site-Scripting conflicts in
browsers

Resources are linked via Hypermedia
• Even though a WADL is provided, Resources may be
dynamically traversed via hrefs. Little prior knowledge of
the service is needed

Result Sets are page able
• All result sets have „next‟, „previous‟ hrefs

What exists right now

• The CTS2 Development Framework
https://github.com/cts2/cts2-framework

• Bioportal -> CTS2 Wrapper
https://github.com/cts2/bioportal-service

• eXist implementation
https://github.com/cts2/exist-service

REST API Signatures

General Pattern:
• Resource by name
/[resourceName]/{resourceId}
• Resource by uri
/[resourceName]byuri?uri={uri}
• List of Resources
/[resourceName]s

REST API Signatures

Sub-resources follow the same pattern
• Resource by name
/[resourceName]/{resourceId}/[subresource]/{id}
• All subresources are linked via hrefs

WADL specification:
http://informatics.mayo.edu/svn/trunk/cts2/spec/ps
m/rest/cts2.wadl

REST API Signatures

Our goal is that by Hypermedia, limited
initial knowledge of the service URL
structure is needed.

In fact, CTS2 QUERY/READ services
function like many services we use
every day

JSON Format
• {"codeSystemCatalogEntry": {
• "codeSystemName": "LNC",
• "designedForOntologyTaskList": [ ],
• "versions": "http://informatics.mayo.edu/cts2/rest/codesystem/LNC/versions",
• "currentVersion": {
• "version": {
• "content": "LNC_232_RRF",
• "href": "http://informatics.mayo.edu/cts2/rest/codesystem/LNC/version/232"
• },
• "codeSystem": {
• "content": "LNC",
• "uri": "http://purl.bioontology.org/ontology/LNC",
• "href": "http://informatics.mayo.edu/cts2/rest/codesystem/LNC"
• }
• },
• "releaseFormatList": [ ],
• "about": "http://purl.bioontology.org/ontology/LNC",
• "formalName": "Logical Observation Identifier Names and Codes",
• "keywordList": [
• "LNC",
• "1350"
• ],
• …

JSON Format (con‟t.)

• Every resource may be returned as
JSON
• Adding a „callback‟ parameter
enables JSONP
callback({"codeSystemVersionCatalogEntry”
{"codeSystemVersionName":"GO_2-0_OBO","versionOf … })

Searching

• Search widget
• Searching for Entities based on a
search string
http://informatics.mayo.edu/cts2widgets/search.html

Searching

• Map Search widget
• Searching ontology mappings based
on queries of either the source or
target
http://informatics.mayo.edu/cts2/rest/widgets/viewmap.html

ChangeSet Workflow

• What is a ChangeSet?
An ordered collection of changes that, when
applied, will transform a service instance
from one consistent state to another. A
ChangeSet is viewed as an atomic unit of
change.

ChangeSet Workflow

• ChangeSets
ChangeSets can be created, committed, and rolled back. They
are similar to a source control branch.

Content in ChangeSets does NOT appear in normal lookups
and queries, although they MAY be included if explicitly asked
for.

ChangeSet Workflow

• Creating a ChangeSet
• Each change set has a unique URI
• ChangeSets start as „OPEN‟

ChangeSet Workflow

• Creating a Resource within a given
ChangeSet
• Any Resource state change must
be within the context of a
ChangeSet

ChangeSet Workflow

• Creating two branches of changes for
the same resource
• The same resource may exist in
different states in different
ChangeSets

ChangeSet Workflow

• Committing a ChangeSet
• Committing a ChangeSet moves
the content of a ChangeSet into
the main service content

ChangeSet Workflow

• Rolling back a ChangeSet
• A rollback will remove all of the
content associated with the
change set, as well as the change
set itself

ChangeSet Workflow

• Creating a Mapping
• A mapping creates relationships
between CodeSystemVersions or
ValueSets

Bioportal Integration

• http://informatics.mayo.edu/cts2widg
ets/widgets.html

But WHY?
• What is this useful for?
There are many well designed REST services out there – do I
use them all? NO!

Our Goal:
A RESTful, Hypermedia based, self describing service that fills a
community need.

The key is whether the data coming back fills a community
need. Users will still use a poorly designed REST service if it
fills a need. Conversely, a perfectly designed RESTful service
that doesn‟t fill a useful need is still not useful.

What need does CTS2 fill?

“Pluto is a Planet”

What is Pluto?

What is a Planet? Is it the International Astronomical Union
definition? Some people have rejected their definition and
defined their own.

Is “Pluto is a Planet” interoperable?


http://purl.bioontology.org/ontology/MSH/D018542

http://purl.bioontology.org/ontology/MSH/D016083

Use-case discussion

Given a Use-case:
• Does the CTS2 Spec include it?
• Do we have tools to do it now?
• If not, could they be created? How?

Resources

http://informatics.mayo.edu/cts2/framework/
See the „In Action‟ section

CTS2 Development Framework In Action

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